RetrogeneDB ID: retro_mmus_2644

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:32479586..32479885(-)
• Located in intron of: ENSMUSG00000014956

Retrocopy information

• Ensembl ID: ENSMUSG00000080753
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hcfc1r1
• Ensembl ID: ENSMUSG00000023904
• Aliases: None
• Description: host cell factor C1 regulator 1 (XPO1-dependent) [Source:MGI Symbol;Acc:MGI:2663619]

Sequence

>retro_mmus_2644
ATGATTCTACAATAGCCACTGGAATGAGGATGCCCTCCAAGTTGGAACAAGTAGGCAACCACTGGGATAACGCTCAGCCT
GGACGCTAGGGAGCCCTTCCACAAGTCGTCCTTGTCCAAGAAGAACATGGTCACCTATTTCTCCTGACTCGACCTACATA
ATGACCAAACTTACTGCAGTCCCCTGTGACTTTTCCCCAAACCCTGTCACTTTGCCCAGAGCTGCTTCTCTGACACTATC
CTAGAAGCCTGATGTGCTGAGGTCAGGAGATACTCCTAGCCTCCACTACCCTGCAACCC

Alignment

ORF - retro_mmus_2644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.19 %
• Parental protein coverage: 88.79 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MILQQPLERG-PPSRDPRATTGVTRGLNAREPLHKQFLSEENMATHFSRLSLHNDHPYCSP-PVTFPEAL
          MILQ.PLE.G.PPS....ATTG.T..L.AREP.HK..LS..NM.T.FS.L.LHND..YCSP.PVTFP..L
Retrocopy MILQ*PLE*GCPPSWNK*ATTGITLSLDAREPFHKSSLSKKNMVTYFS*LDLHNDQTYCSP<PVTFPQTL

Parental  PPLRSPCPELLLWRYPGSLIPEALRLLRLGDTPSP
          ....S.CPELLL..YP.SL.......L....T..P
Retrocopy ----SLCPELLL*HYPRSLMC*GQEILLASTTLQP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.02 RPM	34.95 RPM
SRP007412_cerebellum	0.22 RPM	29.57 RPM
SRP007412_heart	0.09 RPM	49.59 RPM
SRP007412_kidney	0.10 RPM	30.18 RPM
SRP007412_liver	0.00 RPM	14.91 RPM
SRP007412_testis	0.09 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2644 was not detected

EST

No EST(s) were mapped for retro_mmus_2644 retrocopy.

TSS

No TSS is located nearby retro_mmus_2644 retrocopy 5' end.

Lab

retro_mmus_2644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2644 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005504	1 retrocopy	retro_amel_1251,
Callithrix jacchus	ENSCJAG00000015444	1 retrocopy	retro_cjac_1037,
Mus musculus	ENSMUSG00000023904	5 retrocopies	retro_mmus_1485, retro_mmus_1577, retro_mmus_1646, retro_mmus_2644 , retro_mmus_767,